/*
 * Copyright 2006-2018 The MZmine 2 Development Team
 * 
 * This file is part of MZmine 2.
 * 
 * MZmine 2 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 * 
 * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with MZmine 2; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package net.sf.mzmine.modules.peaklistmethods.isotopes.isotopeprediction;

import net.sf.mzmine.datamodel.PolarityType;
import net.sf.mzmine.parameters.UserParameter;
import net.sf.mzmine.parameters.impl.SimpleParameterSet;
import net.sf.mzmine.parameters.parametertypes.ComboParameter;
import net.sf.mzmine.parameters.parametertypes.FormulaParameter;
import net.sf.mzmine.parameters.parametertypes.IntegerParameter;
import net.sf.mzmine.parameters.parametertypes.PercentParameter;
import net.sf.mzmine.parameters.parametertypes.tolerances.MZToleranceParameter;

public class IsotopePatternCalculatorParameters extends SimpleParameterSet {

  public static final FormulaParameter formula = new FormulaParameter();

  public static final MZToleranceParameter mzTolerance = new MZToleranceParameter();

  public static final IntegerParameter charge =
      new IntegerParameter("Charge", "Charge of the molecule (z for calculating m/z values)", 1);

  public static final ComboParameter<PolarityType> polarity = new ComboParameter<PolarityType>(
      "Polarity",
      "Set positive or negative charge of the molecule. Depending on polarity, electron mass is added or removed.",
      PolarityType.values());

  public static final PercentParameter minAbundance = new PercentParameter("Minimum abundance",
      "Minimum abundance of the predicted isotopes", 0.001);

  public IsotopePatternCalculatorParameters() {
    super(new UserParameter[] {formula, charge, polarity, minAbundance});
  }

}
